No abstract

Detection of somatic mutations from late stage solid tumors is a critical part of cancer treatment. Although tumor content is used as a convenient parameter to measure efficacy of detection, it fails to include two basic factors: the lower limit of detection (LLOD), and the ratio of the mutant and wild type allele frequencies.  Recently, the detection of somatic mutations has expanded to liquid biopsy, early stages of cancer and population screening, which all generally carry lower copy numbers of somatic mutations compared to late stage tumors.  With the growing importance of these mutations for targeted chemotherapy and other clinical applications, there is a need re-evaluate the efficacy of detection of somatic mutations.  Hence, a new algorithm, Detection Index (DI), is proposed to standardize the efficacy of all molecular methods and is applicable to all types of clinical samples. Detection Index (DI) is based on two basic determinants: lower limit of detection of the mutant allele, and the ratio of the copies of the mutant allele to that of the wild-type. The benefits of DI include (a) standardization of methods detecting somatic mutations so that laboratory reports will have a uniform interpretation related to clinical picture, and (b) the flexibility to use appropriate amounts of DNA and assay conditions to achieve desired DI.

No abstract

e16591 Background: Routine diagnosis of esophageal cancer varies from locally advanced to metastatic at presentation. Most of these patients are cachectic at presentation and physically not suitable for radical tri-modality treatment as per the CROSS trial. Hence, the prognosis of esophageal cancer remains guarded. Presently, tyrosine kinase inhibitors (TKI) are successfully used in treating melanoma, non-small cell lung cancer, and a possibility for treating esophageal cancer. Allele Specific Multiplex Sequencing (ASMS) detects somatic mutations in samples with low mutant copies and in the presence of overwhelming wild type. Hence, we have re-evaluated and are reporting the findings of the incidence of Braf p.V600E in esophageal cancer using ASMS. Methods: DNA was extracted from 40 formalin fixed paraffin embedded tumor tissue (FFPE) samples that were collected from patients with squamous-cell carcinoma of the esophagus. The Braf p.V600E/K mutations were analyzed using ASMS. All positive results were confirmed by bi-directional ASMS. The results were correlated with patients’ demographic and pathological data. Results: Overall incidence of Braf p.V600E was 92.5% and was present in all stages (IB, IIB, IIIA, IIIB, IIIc and IV) of esophageal cancer. There was no difference in the incidence of Braf p.V600E between patients who smoke, consume alcohol, chew betel or any combination, and those who do not. There is also no gender difference in the incidence of Braf p.V600E. Conclusions: Braf p.V600E is a pivotal driver mutation in the MAPK pathway. Firstly, the data shows incidence of Braf. p.V600E is higher than what is reported in literature and paves the way for follow up with further studies for possible use of TKI targeted chemotherapies. Secondly, incidence of Braf p.V600E mutations could be independent of known cancer etiology (e.g. smoking, consumption of alcohol, chewing betel).